R/downloadPublicSeries.R
In CasedUgr/KnowSeq: KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
Defines functions
downloadPublicSeries
Documented in
downloadPublicSeries
#' Download automatically samples from NCBI/GEO and ArrayExpress public databases.
#'
#' Download automatically samples from series of either microarray and RNA-seq. Furthermore, both NCBI/GEO and ArrayExpress public databases are supported. In the case of Microarray, the raw file are downloaded, if they are available, but for RNA-seq a csv is created with the necessary information to download the samples with the function \code{\link{rawAlignment}}.
#'
#' @param samplesVector A vector which contains the different IDs of the wanted series. These IDs are the IDs of the series from NCBI/GEO or ArrayExpress.
#' @return Nothing to return.
#' @examples
#' downloadPublicSeries(c("GSE74251"))
downloadPublicSeries <- function(samplesVector) {
if(!is.character(samplesVector)){
stop("The parameter passed is wrong. Please, check that the type of the vector be character.")
}else if(length(samplesVector)[1] == 0 || is.null(samplesVector)){
stop("The samplesVector parameter is empty! Please, provide a right geneList.")
}else{
if(dir.exists("ReferenceFiles/")){}else{ system2("mkdir", args = "ReferenceFiles/")}
if(dir.exists("ReferenceFiles/Samples/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/")}
if(dir.exists("ReferenceFiles/Samples/RNAseq/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/RNAseq/")}
if(dir.exists("ReferenceFiles/Samples/RNAseq/BAMFiles/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/RNAseq/BAMFiles/")}
if(dir.exists("ReferenceFiles/Samples/RNAseq/SAMFiles/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/RNAseq/SAMFiles/")}
if(dir.exists("ReferenceFiles/Samples/RNAseq/CountFiles/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/RNAseq/CountFiles/")}
if(dir.exists("ReferenceFiles/Samples/RNAseq/SRAFiles/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/RNAseq/SRAFiles/")}
if(dir.exists("ReferenceFiles/Samples/RNAseq/FASTQFiles/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/RNAseq/FASTQFiles/")}
if(dir.exists("ReferenceFiles/Samples/RNAseq/QuantFiles/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/RNAseq/QuantFiles/")}
for(serie in samplesVector){
if(grepl("GSE",serie)){
cat("\n******************************** NCBI/GEO format detected ********************************\n\n")
webpage <- GET(paste("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=",serie,sep = ""))
webpage_content <- content(webpage, as = "text", encoding = "ISO-8859-1")
webpage <- readLines(tc <- textConnection(webpage_content)); close(tc)
pagetree <- htmlTreeParse(webpage, error=function(...){}, useInternalNodes = TRUE)
# parse the tree by tables
x <- xpathSApply(pagetree, "//*/table", xmlValue)
# do some clean up with regular expressions
x <- unlist(strsplit(x, "\n"))
x <- gsub("\t","",x)
x <- sub("^[[:space:]]*(.*?)[[:space:]]*$", "\\1", x, perl=TRUE)
x <- x[!(x %in% c("", "|"))]
if(any(grepl("Expression profiling by array", x))){
cat("******************************** MICROARRAY series detected *******************************\n\n")
cat(paste("Searching the RAW data from the microarray series ",serie,"\n",sep = ""))
if(!http_error(paste("ftp://ftp.ncbi.nlm.nih.gov/geo/series/",substring(serie,1,nchar(serie)-3),"nnn/",serie,"/suppl/",serie,"_RAW.tar",sep = ""))){
cat("The RAW data have been found correctly...\n")
POST(paste("ftp://ftp.ncbi.nlm.nih.gov/geo/series/",substring(serie,1,nchar(serie)-3),"nnn/",serie,"/suppl/",serie,"_RAW.tar",sep = ""), write_disk(paste(serie,"_RAW.tar",sep = ""), overwrite=TRUE))
cat(paste("Decompressing ", serie,"_RAW.tar...\n",sep=""))
if(dir.exists("ReferenceFiles/Samples")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/")}
if(dir.exists("ReferenceFiles/Samples/Microarray/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/Microarray/")}
fileMove(from = paste(serie,"_RAW.tar",sep = ""),
to = paste("ReferenceFiles/Samples/Microarray/",serie,"/",serie,"_RAW.tar",sep = ""))
if(dir.exists(paste("ReferenceFiles/Samples/Microarray/",serie,sep=""))){}else{ system2("mkdir", args = paste("ReferenceFiles/Samples/Microarray/",serie,sep=""))}
system2("tar", args = paste("-xf ReferenceFiles/Samples/Microarray/", serie,"/",serie,"_RAW.tar -C ", "ReferenceFiles/Samples/Microarray/",serie,sep = ""))
system2("rm", args = paste("ReferenceFiles/Samples/Microarray/", serie,"/",serie,"_RAW.tar",sep = ""))
CELFiles <- list.files(paste("ReferenceFiles/Samples/Microarray/",serie,"/",sep=""))
for(CEL in CELFiles){
cat(paste("Decompressing ", CEL, " file...\n",sep=""))
system2("gzip", args = paste("-d ReferenceFiles/Samples/Microarray/",serie,"/",CEL,sep = ""))
}
}else{
cat("There aren't RAW data available for this series or the series doesn't exist\n")
}
}else if(any(grepl("Expression profiling by high throughput sequencing", x))){
cat("******************************** RNA-SEQ series detected ********************************\n\n")
cat(paste("Building the CSV file for RNA-seq samples for series ",serie,"\n",sep = ""))
gsmList <- unique(x[grep("\\bGSM.*\\d", x)])
Run = character()
download_path = character()
LibraryLayout = character()
i = 1
for(gsm in gsmList){
webpage <- GET(paste("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=",gsm,sep = ""))
webpage_content <- content(webpage, as = "text", encoding = "ISO-8859-1")
webpage <- readLines(tc <- textConnection(webpage_content)); close(tc)
pagetree <- htmlTreeParse(webpage, error=function(...){}, useInternalNodes = TRUE)
# parse the tree by tables
xx <- xpathSApply(pagetree, "//*/table", xmlValue)
# do some clean up with regular expressions
xx <- unlist(strsplit(xx, "\n"))
xx <- gsub("\t","",xx)
xx <- sub("^[[:space:]]*(.*?)[[:space:]]*$", "\\1", xx, perl=TRUE)
xx <- xx[!(xx %in% c("", "|"))]
srxID <- unique(unlist(xx[grep("\\bSRX.*\\d", xx)])[1])
webpage <- GET(paste("https://www.ncbi.nlm.nih.gov/sra?term=",srxID,sep = ""))
webpage_content <- content(webpage, as = "text", encoding = "ISO-8859-1")
webpage.treated <- readLines(tc <- textConnection(webpage_content)); close(tc)
pagetree <- htmlTreeParse(webpage.treated, error=function(...){}, useInternalNodes = TRUE)
# parse the tree by tables
xxx <- xpathSApply(pagetree, "//*/table", xmlValue)
# do some clean up with regular expressions
xxx <- unlist(strsplit(xxx, "\n"))
xxx <- gsub("\t","",xxx)
xxx <- sub("^[[:space:]]*(.*?)[[:space:]]*$", "\\1", xxx, perl=TRUE)
xxx <- xxx[!(xxx %in% c("", "|"))]
LibraryLayoutElement = ""
RunElement = ""
if(grepl("<span>SINGLE</span>",webpage)){
LibraryLayoutElement = "SINGLE"
}else if(grepl("<span>PAIRED</span>",webpage)){
LibraryLayoutElement = "PAIRED"
}
m <- gregexpr("\\brun=SRR(.*?)\"", webpage_content)
regx <- regmatches(webpage_content,m)
RunElement <- as.character(unlist(regx))
m <- gregexpr("\\bSRP/.*\\d", x)
regx <- regmatches(x,m)
if(length(RunElement)==1){
RunElement <- substr(RunElement,5,nchar(RunElement))
RunElement <- substr(RunElement,1,nchar(RunElement)-1)
Run[i] <- RunElement
downloadpath = paste("ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/",substr(RunElement,1,6),"/",RunElement,"/",RunElement,".sra",sep = "")
download_path[i] <- downloadpath
LibraryLayout[i] <- LibraryLayoutElement
i = i + 1
}else{
RunElement[1] <- substr(RunElement[1],5,nchar(RunElement[1]))
RunElement[1] <- substr(RunElement[1],1,nchar(RunElement[1])-1)
Run[i] <- RunElement[1]
downloadpath = paste("ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/",substr(RunElement[1],1,6),"/",RunElement[1],"/",RunElement[1],".sra",sep = "")
download_path[i] <- downloadpath
LibraryLayout[i] <- LibraryLayoutElement
RunElement[2] <- substr(RunElement[2],5,nchar(RunElement[2]))
RunElement[2] <- substr(RunElement[2],1,nchar(RunElement[2])-1)
Run[i+1] <- RunElement[2]
downloadpath = paste("ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/",substr(RunElement[2],1,6),"/",RunElement[2],"/",RunElement[2],".sra",sep = "")
download_path[i+1] <- downloadpath
LibraryLayout[i+1] <- LibraryLayoutElement
i = i + 2
}
}
rnaseq.data <- data.frame(Run, LibraryLayout, download_path)
cat("Exporting CSV to ReferenceFiles folder...")
write.csv(rnaseq.data,paste("ReferenceFiles/",serie,".csv",sep = ""))
}
}else if(grepl("E-",serie)){
cat("\n******************************** ArrayExpress format detected ********************************\n\n")
webpage <- GET(paste("https://www.ebi.ac.uk/arrayexpress/experiments/",serie,"/",sep = ""))
webpage_content <- content(webpage, as = "text", encoding = "ISO-8859-1")
webpage <- readLines(tc <- textConnection(webpage_content)); close(tc)
pagetree <- htmlTreeParse(webpage, error=function(...){}, useInternalNodes = TRUE)
# parse the tree by tables
x <- xpathSApply(pagetree, "//*/table", xmlValue)
# do some clean up with regular expressions
x <- unlist(strsplit(x, "\n"))
x <- gsub("\t","",x)
x <- sub("^[[:space:]]*(.*?)[[:space:]]*$", "\\1", x, perl=TRUE)
x <- x[!(x %in% c("", "|"))]
if(any(grepl("transcription profiling by array", x))){
cat("******************************** MICROARRAY series detected *******************************\n\n")
cat(paste("Searching the RAW data from the microarray series ",serie,"\n",sep = ""))
if(any(grepl("\\braw\\b",x))){
cat("The RAW data have been found correctly...\n")
m <- gregexpr("\\bE-MTAB(.*?)zip", x)
regx <- regmatches(x,m)
regx <- unlist(regx)
regx <- unique(regx)
for(raw in regx){
cat(paste("https://www.ebi.ac.uk/arrayexpress/files/",serie,"/",raw,"\n",sep = ""))
POST(paste("https://www.ebi.ac.uk/arrayexpress/files/",serie,"/",raw,sep = ""), write_disk(raw), overwrite=TRUE)
cat(paste("Decompressing ",raw,"\n",sep=""))
if(dir.exists("ReferenceFiles/Samples")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/")}
if(dir.exists("ReferenceFiles/Samples/Microarray/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/Microarray/")}
if(dir.exists(paste("ReferenceFiles/Samples/Microarray/",serie,sep=""))){}else{ system2("mkdir", args = paste("ReferenceFiles/Samples/Microarray/",serie,sep=""))}
fileMove(from = paste(raw,sep = ""),
to = paste("ReferenceFiles/Samples/Microarray/",serie,"/",raw,sep = ""))
}
}else{
cat("There aren't RAW data available for this series or the series doesn't exist\n")
}
}else if(any(grepl("RNA-seq of coding RNA", x))){
cat("******************************** RNA-SEQ series detected ********************************\n\n")
if(grepl(paste(serie,".sdrf.txt",sep = ""),x[1])){
cat("Downloading the sdrf.txt and converting to TSV...\n")
POST(paste("https://www.ebi.ac.uk/arrayexpress/files/",serie,"/",serie,".sdrf.txt",sep = ""), write_disk(paste(serie,".sdrf.txt",sep = "")), overwrite=TRUE)
fileMove(from = paste(serie,".sdrf.txt",sep = ""),
to = paste("ReferenceFiles/",serie,".tsv",sep = ""))
}else{
cat("There isn't any sdrf file available for this series or the series doesn't exist\n")
}
}
}else{
stop("The IDs of the series doesn't exist or it's not supported. Please, try again with NCBI/GEO and ArrayExpress IDs\n")
}
}
}
}
CasedUgr/KnowSeq documentation built on Aug. 16, 2022, 6:19 a.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions downloadPublicSeries
Documented in downloadPublicSeries
#' Download automatically samples from NCBI/GEO and ArrayExpress public databases.
#'
#' Download automatically samples from series of either microarray and RNA-seq. Furthermore, both NCBI/GEO and ArrayExpress public databases are supported. In the case of Microarray, the raw file are downloaded, if they are available, but for RNA-seq a csv is created with the necessary information to download the samples with the function \code{\link{rawAlignment}}.
#'
#' @param samplesVector A vector which contains the different IDs of the wanted series. These IDs are the IDs of the series from NCBI/GEO or ArrayExpress.
#' @return Nothing to return.
#' @examples
#' downloadPublicSeries(c("GSE74251"))
downloadPublicSeries <- function(samplesVector) {
if(!is.character(samplesVector)){
stop("The parameter passed is wrong. Please, check that the type of the vector be character.")
}else if(length(samplesVector)[1] == 0 || is.null(samplesVector)){
stop("The samplesVector parameter is empty! Please, provide a right geneList.")
}else{
if(dir.exists("ReferenceFiles/")){}else{ system2("mkdir", args = "ReferenceFiles/")}
if(dir.exists("ReferenceFiles/Samples/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/")}
if(dir.exists("ReferenceFiles/Samples/RNAseq/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/RNAseq/")}
if(dir.exists("ReferenceFiles/Samples/RNAseq/BAMFiles/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/RNAseq/BAMFiles/")}
if(dir.exists("ReferenceFiles/Samples/RNAseq/SAMFiles/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/RNAseq/SAMFiles/")}
if(dir.exists("ReferenceFiles/Samples/RNAseq/CountFiles/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/RNAseq/CountFiles/")}
if(dir.exists("ReferenceFiles/Samples/RNAseq/SRAFiles/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/RNAseq/SRAFiles/")}
if(dir.exists("ReferenceFiles/Samples/RNAseq/FASTQFiles/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/RNAseq/FASTQFiles/")}
if(dir.exists("ReferenceFiles/Samples/RNAseq/QuantFiles/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/RNAseq/QuantFiles/")}
for(serie in samplesVector){
if(grepl("GSE",serie)){
cat("\n******************************** NCBI/GEO format detected ********************************\n\n")
webpage <- GET(paste("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=",serie,sep = ""))
webpage_content <- content(webpage, as = "text", encoding = "ISO-8859-1")
webpage <- readLines(tc <- textConnection(webpage_content)); close(tc)
pagetree <- htmlTreeParse(webpage, error=function(...){}, useInternalNodes = TRUE)
# parse the tree by tables
x <- xpathSApply(pagetree, "//*/table", xmlValue)
# do some clean up with regular expressions
x <- unlist(strsplit(x, "\n"))
x <- gsub("\t","",x)
x <- sub("^[[:space:]]*(.*?)[[:space:]]*$", "\\1", x, perl=TRUE)
x <- x[!(x %in% c("", "|"))]
if(any(grepl("Expression profiling by array", x))){
cat("******************************** MICROARRAY series detected *******************************\n\n")
cat(paste("Searching the RAW data from the microarray series ",serie,"\n",sep = ""))
if(!http_error(paste("ftp://ftp.ncbi.nlm.nih.gov/geo/series/",substring(serie,1,nchar(serie)-3),"nnn/",serie,"/suppl/",serie,"_RAW.tar",sep = ""))){
cat("The RAW data have been found correctly...\n")
POST(paste("ftp://ftp.ncbi.nlm.nih.gov/geo/series/",substring(serie,1,nchar(serie)-3),"nnn/",serie,"/suppl/",serie,"_RAW.tar",sep = ""), write_disk(paste(serie,"_RAW.tar",sep = ""), overwrite=TRUE))
cat(paste("Decompressing ", serie,"_RAW.tar...\n",sep=""))
if(dir.exists("ReferenceFiles/Samples")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/")}
if(dir.exists("ReferenceFiles/Samples/Microarray/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/Microarray/")}
fileMove(from = paste(serie,"_RAW.tar",sep = ""),
to = paste("ReferenceFiles/Samples/Microarray/",serie,"/",serie,"_RAW.tar",sep = ""))
if(dir.exists(paste("ReferenceFiles/Samples/Microarray/",serie,sep=""))){}else{ system2("mkdir", args = paste("ReferenceFiles/Samples/Microarray/",serie,sep=""))}
system2("tar", args = paste("-xf ReferenceFiles/Samples/Microarray/", serie,"/",serie,"_RAW.tar -C ", "ReferenceFiles/Samples/Microarray/",serie,sep = ""))
system2("rm", args = paste("ReferenceFiles/Samples/Microarray/", serie,"/",serie,"_RAW.tar",sep = ""))
CELFiles <- list.files(paste("ReferenceFiles/Samples/Microarray/",serie,"/",sep=""))
for(CEL in CELFiles){
cat(paste("Decompressing ", CEL, " file...\n",sep=""))
system2("gzip", args = paste("-d ReferenceFiles/Samples/Microarray/",serie,"/",CEL,sep = ""))
}
}else{
cat("There aren't RAW data available for this series or the series doesn't exist\n")
}
}else if(any(grepl("Expression profiling by high throughput sequencing", x))){
cat("******************************** RNA-SEQ series detected ********************************\n\n")
cat(paste("Building the CSV file for RNA-seq samples for series ",serie,"\n",sep = ""))
gsmList <- unique(x[grep("\\bGSM.*\\d", x)])
Run = character()
download_path = character()
LibraryLayout = character()
i = 1
for(gsm in gsmList){
webpage <- GET(paste("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=",gsm,sep = ""))
webpage_content <- content(webpage, as = "text", encoding = "ISO-8859-1")
webpage <- readLines(tc <- textConnection(webpage_content)); close(tc)
pagetree <- htmlTreeParse(webpage, error=function(...){}, useInternalNodes = TRUE)
# parse the tree by tables
xx <- xpathSApply(pagetree, "//*/table", xmlValue)
# do some clean up with regular expressions
xx <- unlist(strsplit(xx, "\n"))
xx <- gsub("\t","",xx)
xx <- sub("^[[:space:]]*(.*?)[[:space:]]*$", "\\1", xx, perl=TRUE)
xx <- xx[!(xx %in% c("", "|"))]
srxID <- unique(unlist(xx[grep("\\bSRX.*\\d", xx)])[1])
webpage <- GET(paste("https://www.ncbi.nlm.nih.gov/sra?term=",srxID,sep = ""))
webpage_content <- content(webpage, as = "text", encoding = "ISO-8859-1")
webpage.treated <- readLines(tc <- textConnection(webpage_content)); close(tc)
pagetree <- htmlTreeParse(webpage.treated, error=function(...){}, useInternalNodes = TRUE)
# parse the tree by tables
xxx <- xpathSApply(pagetree, "//*/table", xmlValue)
# do some clean up with regular expressions
xxx <- unlist(strsplit(xxx, "\n"))
xxx <- gsub("\t","",xxx)
xxx <- sub("^[[:space:]]*(.*?)[[:space:]]*$", "\\1", xxx, perl=TRUE)
xxx <- xxx[!(xxx %in% c("", "|"))]
LibraryLayoutElement = ""
RunElement = ""
if(grepl("<span>SINGLE</span>",webpage)){
LibraryLayoutElement = "SINGLE"
}else if(grepl("<span>PAIRED</span>",webpage)){
LibraryLayoutElement = "PAIRED"
}
m <- gregexpr("\\brun=SRR(.*?)\"", webpage_content)
regx <- regmatches(webpage_content,m)
RunElement <- as.character(unlist(regx))
m <- gregexpr("\\bSRP/.*\\d", x)
regx <- regmatches(x,m)
if(length(RunElement)==1){
RunElement <- substr(RunElement,5,nchar(RunElement))
RunElement <- substr(RunElement,1,nchar(RunElement)-1)
Run[i] <- RunElement
downloadpath = paste("ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/",substr(RunElement,1,6),"/",RunElement,"/",RunElement,".sra",sep = "")
download_path[i] <- downloadpath
LibraryLayout[i] <- LibraryLayoutElement
i = i + 1
}else{
RunElement[1] <- substr(RunElement[1],5,nchar(RunElement[1]))
RunElement[1] <- substr(RunElement[1],1,nchar(RunElement[1])-1)
Run[i] <- RunElement[1]
downloadpath = paste("ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/",substr(RunElement[1],1,6),"/",RunElement[1],"/",RunElement[1],".sra",sep = "")
download_path[i] <- downloadpath
LibraryLayout[i] <- LibraryLayoutElement
RunElement[2] <- substr(RunElement[2],5,nchar(RunElement[2]))
RunElement[2] <- substr(RunElement[2],1,nchar(RunElement[2])-1)
Run[i+1] <- RunElement[2]
downloadpath = paste("ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/",substr(RunElement[2],1,6),"/",RunElement[2],"/",RunElement[2],".sra",sep = "")
download_path[i+1] <- downloadpath
LibraryLayout[i+1] <- LibraryLayoutElement
i = i + 2
}
}
rnaseq.data <- data.frame(Run, LibraryLayout, download_path)
cat("Exporting CSV to ReferenceFiles folder...")
write.csv(rnaseq.data,paste("ReferenceFiles/",serie,".csv",sep = ""))
}
}else if(grepl("E-",serie)){
cat("\n******************************** ArrayExpress format detected ********************************\n\n")
webpage <- GET(paste("https://www.ebi.ac.uk/arrayexpress/experiments/",serie,"/",sep = ""))
webpage_content <- content(webpage, as = "text", encoding = "ISO-8859-1")
webpage <- readLines(tc <- textConnection(webpage_content)); close(tc)
pagetree <- htmlTreeParse(webpage, error=function(...){}, useInternalNodes = TRUE)
# parse the tree by tables
x <- xpathSApply(pagetree, "//*/table", xmlValue)
# do some clean up with regular expressions
x <- unlist(strsplit(x, "\n"))
x <- gsub("\t","",x)
x <- sub("^[[:space:]]*(.*?)[[:space:]]*$", "\\1", x, perl=TRUE)
x <- x[!(x %in% c("", "|"))]
if(any(grepl("transcription profiling by array", x))){
cat("******************************** MICROARRAY series detected *******************************\n\n")
cat(paste("Searching the RAW data from the microarray series ",serie,"\n",sep = ""))
if(any(grepl("\\braw\\b",x))){
cat("The RAW data have been found correctly...\n")
m <- gregexpr("\\bE-MTAB(.*?)zip", x)
regx <- regmatches(x,m)
regx <- unlist(regx)
regx <- unique(regx)
for(raw in regx){
cat(paste("https://www.ebi.ac.uk/arrayexpress/files/",serie,"/",raw,"\n",sep = ""))
POST(paste("https://www.ebi.ac.uk/arrayexpress/files/",serie,"/",raw,sep = ""), write_disk(raw), overwrite=TRUE)
cat(paste("Decompressing ",raw,"\n",sep=""))
if(dir.exists("ReferenceFiles/Samples")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/")}
if(dir.exists("ReferenceFiles/Samples/Microarray/")){}else{ system2("mkdir", args = "ReferenceFiles/Samples/Microarray/")}
if(dir.exists(paste("ReferenceFiles/Samples/Microarray/",serie,sep=""))){}else{ system2("mkdir", args = paste("ReferenceFiles/Samples/Microarray/",serie,sep=""))}
fileMove(from = paste(raw,sep = ""),
to = paste("ReferenceFiles/Samples/Microarray/",serie,"/",raw,sep = ""))
}
}else{
cat("There aren't RAW data available for this series or the series doesn't exist\n")
}
}else if(any(grepl("RNA-seq of coding RNA", x))){
cat("******************************** RNA-SEQ series detected ********************************\n\n")
if(grepl(paste(serie,".sdrf.txt",sep = ""),x[1])){
cat("Downloading the sdrf.txt and converting to TSV...\n")
POST(paste("https://www.ebi.ac.uk/arrayexpress/files/",serie,"/",serie,".sdrf.txt",sep = ""), write_disk(paste(serie,".sdrf.txt",sep = "")), overwrite=TRUE)
fileMove(from = paste(serie,".sdrf.txt",sep = ""),
to = paste("ReferenceFiles/",serie,".tsv",sep = ""))
}else{
cat("There isn't any sdrf file available for this series or the series doesn't exist\n")
}
}
}else{
stop("The IDs of the series doesn't exist or it's not supported. Please, try again with NCBI/GEO and ArrayExpress IDs\n")
}
}
}
}
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